Abstract Prospective Functional Characterization of All Possible Missense Variants in HNF1A Loss-of-function mutations in HNF1A are the most common cause of maturity-onset diabetes of the young (MODY). Individuals with HNF1A-MODY benefit from specific pharmacotherapy with low dose sulfonylureas and can avoid insulin injections, but distinguishing these patients from those with polygenic type 2 diabetes (T2D) on clinical grounds is challenging. Gene sequencing of HNF1A in population-sized cohorts demonstrates that ~1:50 individuals with diabetes harbors a missense variant in HNF1A. But almost all of these are novel, of unknown functional consequence, and therefore clinically unactionable. In just the past few years, dozens of novel variants in HNF1A have been identified, overwhelming the capacity of clinical laboratories to functionally characterize them. We hypothesize that the ability to functionally characterize variants at the rate and scale they are now being discovered would enable diagnoses and potentially guide therapy for thousands of HNF1A variant carriers. To address these challenges, we propose a prospective experimental approach: 1) In order to establish the function of any missense variant in HNF1A that may be found in future genome sequencing, we will engineer every possible amino acid substitution and measure HNF1A function in a disease-relevant bioassays. 2) In order to relate HNF1A function to diabetes risk and therapeutic response we will correlate molecular function in vitro with clinical phenotypes of ~2000 HNF1A missense variant carriers in vivo. If successful, our pilot study will allow instant functional classification of any missense variant in HNF1A that may be found in clinical or investigational sequencing. The data generated will lay the foundation for future recruit- by-genotype trials to assess sulfonylurea responsiveness in diabetic patients carrying HNF1A missense variants.